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Items: 1 to 50 of 61

1.

Multiplex genome editing of microorganisms using CRISPR-Cas.

Adiego-Pérez B, Randazzo P, Daran JM, Verwaal R, Roubos JA, Daran-Lapujade P, van der Oost J.

FEMS Microbiol Lett. 2019 Apr 1;366(8). pii: fnz086. doi: 10.1093/femsle/fnz086.

2.

The Genetic Makeup and Expression of the Glycolytic and Fermentative Pathways Are Highly Conserved Within the Saccharomyces Genus.

Boonekamp FJ, Dashko S, van den Broek M, Gehrmann T, Daran JM, Daran-Lapujade P.

Front Genet. 2018 Nov 16;9:504. doi: 10.3389/fgene.2018.00504. eCollection 2018.

3.

The Crabtree Effect Shapes the Saccharomyces cerevisiae Lag Phase during the Switch between Different Carbon Sources.

Perez-Samper G, Cerulus B, Jariani A, Vermeersch L, Barrajón Simancas N, Bisschops MMM, van den Brink J, Solis-Escalante D, Gallone B, De Maeyer D, van Bael E, Wenseleers T, Michiels J, Marchal K, Daran-Lapujade P, Verstrepen KJ.

MBio. 2018 Oct 30;9(5). pii: e01331-18. doi: 10.1128/mBio.01331-18.

4.

A toolkit for rapid CRISPR-SpCas9 assisted construction of hexose-transport-deficient Saccharomyces cerevisiae strains.

Wijsman M, Swiat MA, Marques WL, Hettinga JK, van den Broek M, Torre Cortés P, Mans R, Pronk JT, Daran JM, Daran-Lapujade P.

FEMS Yeast Res. 2019 Jan 1;19(1). doi: 10.1093/femsyr/foy107.

5.

A protocol for introduction of multiple genetic modifications in Saccharomyces cerevisiae using CRISPR/Cas9.

Mans R, Wijsman M, Daran-Lapujade P, Daran JM.

FEMS Yeast Res. 2018 Nov 1;18(7). doi: 10.1093/femsyr/foy063.

6.

FnCpf1: a novel and efficient genome editing tool for Saccharomyces cerevisiae.

Swiat MA, Dashko S, den Ridder M, Wijsman M, van der Oost J, Daran JM, Daran-Lapujade P.

Nucleic Acids Res. 2017 Dec 1;45(21):12585-12598. doi: 10.1093/nar/gkx1007.

7.

Pathway swapping: Toward modular engineering of essential cellular processes.

Kuijpers NG, Solis-Escalante D, Luttik MA, Bisschops MM, Boonekamp FJ, van den Broek M, Pronk JT, Daran JM, Daran-Lapujade P.

Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15060-15065. doi: 10.1073/pnas.1606701113. Epub 2016 Dec 12.

8.

Extreme calorie restriction in yeast retentostats induces uniform non-quiescent growth arrest.

Bisschops MM, Luttik MA, Doerr A, Verheijen PJ, Bruggeman F, Pronk JT, Daran-Lapujade P.

Biochim Biophys Acta Mol Cell Res. 2017 Jan;1864(1):231-242. doi: 10.1016/j.bbamcr.2016.11.002. Epub 2016 Nov 4.

9.

Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates.

Vos T, Hakkaart XD, de Hulster EA, van Maris AJ, Pronk JT, Daran-Lapujade P.

Microb Cell Fact. 2016 Jun 17;15(1):111. doi: 10.1186/s12934-016-0501-z.

10.

Pichia pastoris Exhibits High Viability and a Low Maintenance Energy Requirement at Near-Zero Specific Growth Rates.

Rebnegger C, Vos T, Graf AB, Valli M, Pronk JT, Daran-Lapujade P, Mattanovich D.

Appl Environ Microbiol. 2016 Jul 15;82(15):4570-4583. doi: 10.1128/AEM.00638-16. Print 2016 Aug 1.

11.

Oxygen availability strongly affects chronological lifespan and thermotolerance in batch cultures of Saccharomyces cerevisiae.

Bisschops MM, Vos T, Martínez-Moreno R, Cortés PT, Pronk JT, Daran-Lapujade P.

Microb Cell. 2015 Oct 21;2(11):429-444. doi: 10.15698/mic2015.11.238.

12.

Growth-rate dependency of de novo resveratrol production in chemostat cultures of an engineered Saccharomyces cerevisiae strain.

Vos T, de la Torre Cortés P, van Gulik WM, Pronk JT, Daran-Lapujade P.

Microb Cell Fact. 2015 Sep 14;14:133. doi: 10.1186/s12934-015-0321-6.

13.

A Minimal Set of Glycolytic Genes Reveals Strong Redundancies in Saccharomyces cerevisiae Central Metabolism.

Solis-Escalante D, Kuijpers NG, Barrajon-Simancas N, van den Broek M, Pronk JT, Daran JM, Daran-Lapujade P.

Eukaryot Cell. 2015 Aug;14(8):804-16. doi: 10.1128/EC.00064-15. Epub 2015 Jun 12.

14.

Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates.

Ercan O, Bisschops MM, Overkamp W, Jørgensen TR, Ram AF, Smid EJ, Pronk JT, Kuipers OP, Daran-Lapujade P, Kleerebezem M.

Appl Environ Microbiol. 2015 Sep 1;81(17):5662-70. doi: 10.1128/AEM.00944-15. Epub 2015 Jun 5. Review.

15.

S. cerevisiae × S. eubayanus interspecific hybrid, the best of both worlds and beyond.

Hebly M, Brickwedde A, Bolat I, Driessen MR, de Hulster EA, van den Broek M, Pronk JT, Geertman JM, Daran JM, Daran-Lapujade P.

FEMS Yeast Res. 2015 May;15(3). pii: fov005. doi: 10.1093/femsyr/fov005. Epub 2015 Mar 4.

PMID:
25743788
16.

CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae.

Mans R, van Rossum HM, Wijsman M, Backx A, Kuijpers NG, van den Broek M, Daran-Lapujade P, Pronk JT, van Maris AJ, Daran JM.

FEMS Yeast Res. 2015 Mar;15(2). pii: fov004. doi: 10.1093/femsyr/fov004. Epub 2015 Mar 4.

17.

The genome sequence of the popular hexose-transport-deficient Saccharomyces cerevisiae strain EBY.VW4000 reveals LoxP/Cre-induced translocations and gene loss.

Solis-Escalante D, van den Broek M, Kuijpers NG, Pronk JT, Boles E, Daran JM, Daran-Lapujade P.

FEMS Yeast Res. 2015 Mar;15(2). pii: fou004. doi: 10.1093/femsyr/fou004.

PMID:
25673752
18.

Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures.

Binai NA, Bisschops MM, van Breukelen B, Mohammed S, Loeff L, Pronk JT, Heck AJ, Daran-Lapujade P, Slijper M.

J Proteome Res. 2014 Aug 1;13(8):3542-53. doi: 10.1021/pr5003388. Epub 2014 Jul 18.

PMID:
25000127
19.

Efficient simultaneous excision of multiple selectable marker cassettes using I-SceI-induced double-strand DNA breaks in Saccharomyces cerevisiae.

Solis-Escalante D, Kuijpers NG, van der Linden FH, Pronk JT, Daran JM, Daran-Lapujade P.

FEMS Yeast Res. 2014 Aug;14(5):741-54. doi: 10.1111/1567-1364.12162. Epub 2014 Jun 27.

20.

Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles.

Hebly M, de Ridder D, de Hulster EA, de la Torre Cortes P, Pronk JT, Daran-Lapujade P.

Appl Environ Microbiol. 2014 Jul;80(14):4433-49. doi: 10.1128/AEM.00785-14. Epub 2014 May 9.

21.

To divide or not to divide: a key role of Rim15 in calorie-restricted yeast cultures.

Bisschops MM, Zwartjens P, Keuter SG, Pronk JT, Daran-Lapujade P.

Biochim Biophys Acta. 2014 May;1843(5):1020-30. doi: 10.1016/j.bbamcr.2014.01.026. Epub 2014 Jan 31.

22.

One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae.

Kuijpers NG, Chroumpi S, Vos T, Solis-Escalante D, Bosman L, Pronk JT, Daran JM, Daran-Lapujade P.

FEMS Yeast Res. 2013 Dec;13(8):769-81. doi: 10.1111/1567-1364.12087. Epub 2013 Oct 7.

23.

Transcriptome-based characterization of interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat cocultures.

Mendes F, Sieuwerts S, de Hulster E, Almering MJ, Luttik MA, Pronk JT, Smid EJ, Bron PA, Daran-Lapujade P.

Appl Environ Microbiol. 2013 Oct;79(19):5949-61. doi: 10.1128/AEM.01115-13. Epub 2013 Jul 19.

24.

A versatile, efficient strategy for assembly of multi-fragment expression vectors in Saccharomyces cerevisiae using 60 bp synthetic recombination sequences.

Kuijpers NG, Solis-Escalante D, Bosman L, van den Broek M, Pronk JT, Daran JM, Daran-Lapujade P.

Microb Cell Fact. 2013 May 10;12:47. doi: 10.1186/1475-2859-12-47.

25.

amdSYM, a new dominant recyclable marker cassette for Saccharomyces cerevisiae.

Solis-Escalante D, Kuijpers NG, Bongaerts N, Bolat I, Bosman L, Pronk JT, Daran JM, Daran-Lapujade P.

FEMS Yeast Res. 2013 Feb;13(1):126-39. doi: 10.1111/1567-1364.12024. Epub 2012 Dec 17.

26.

Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics?

Cruz LA, Hebly M, Duong GH, Wahl SA, Pronk JT, Heijnen JJ, Daran-Lapujade P, van Gulik WM.

BMC Syst Biol. 2012 Dec 7;6:151. doi: 10.1186/1752-0509-6-151.

27.

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology.

Nijkamp JF, van den Broek M, Datema E, de Kok S, Bosman L, Luttik MA, Daran-Lapujade P, Vongsangnak W, Nielsen J, Heijne WH, Klaassen P, Paddon CJ, Platt D, Kötter P, van Ham RC, Reinders MJ, Pronk JT, de Ridder D, Daran JM.

Microb Cell Fact. 2012 Mar 26;11:36. doi: 10.1186/1475-2859-11-36.

28.

Cellular responses of Saccharomyces cerevisiae at near-zero growth rates: transcriptome analysis of anaerobic retentostat cultures.

Boender LG, van Maris AJ, de Hulster EA, Almering MJ, van der Klei IJ, Veenhuis M, de Winde JH, Pronk JT, Daran-Lapujade P.

FEMS Yeast Res. 2011 Dec;11(8):603-20. doi: 10.1111/j.1567-1364.2011.00750.x. Epub 2011 Sep 26.

29.

The diversity of protein turnover and abundance under nitrogen-limited steady-state conditions in Saccharomyces cerevisiae.

Helbig AO, Daran-Lapujade P, van Maris AJ, de Hulster EA, de Ridder D, Pronk JT, Heck AJ, Slijper M.

Mol Biosyst. 2011 Dec;7(12):3316-26. doi: 10.1039/c1mb05250k. Epub 2011 Oct 10.

PMID:
21984188
30.

Extreme calorie restriction and energy source starvation in Saccharomyces cerevisiae represent distinct physiological states.

Boender LG, Almering MJ, Dijk M, van Maris AJ, de Winde JH, Pronk JT, Daran-Lapujade P.

Biochim Biophys Acta. 2011 Dec;1813(12):2133-44. doi: 10.1016/j.bbamcr.2011.07.008. Epub 2011 Jul 22.

31.

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.

Canelas AB, Harrison N, Fazio A, Zhang J, Pitkänen JP, van den Brink J, Bakker BM, Bogner L, Bouwman J, Castrillo JI, Cankorur A, Chumnanpuen P, Daran-Lapujade P, Dikicioglu D, van Eunen K, Ewald JC, Heijnen JJ, Kirdar B, Mattila I, Mensonides FI, Niebel A, Penttilä M, Pronk JT, Reuss M, Salusjärvi L, Sauer U, Sherman D, Siemann-Herzberg M, Westerhoff H, de Winde J, Petranovic D, Oliver SG, Workman CT, Zamboni N, Nielsen J.

Nat Commun. 2010;1:145. doi: 10.1038/ncomms1150.

PMID:
21266995
32.

Predicting metabolic fluxes using gene expression differences as constraints.

van Berlo RJ, de Ridder D, Daran JM, Daran-Lapujade PA, Teusink B, Reinders MJ.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):206-16. doi: 10.1109/TCBB.2009.55.

PMID:
21071808
33.

Measuring enzyme activities under standardized in vivo-like conditions for systems biology.

van Eunen K, Bouwman J, Daran-Lapujade P, Postmus J, Canelas AB, Mensonides FI, Orij R, Tuzun I, van den Brink J, Smits GJ, van Gulik WM, Brul S, Heijnen JJ, de Winde JH, de Mattos MJ, Kettner C, Nielsen J, Westerhoff HV, Bakker BM.

FEBS J. 2010 Feb;277(3):749-60. doi: 10.1111/j.1742-4658.2009.07524.x. Epub 2010 Jan 7.

34.

A three-way proteomics strategy allows differential analysis of yeast mitochondrial membrane protein complexes under anaerobic and aerobic conditions.

Helbig AO, de Groot MJ, van Gestel RA, Mohammed S, de Hulster EA, Luttik MA, Daran-Lapujade P, Pronk JT, Heck AJ, Slijper M.

Proteomics. 2009 Oct;9(20):4787-98. doi: 10.1002/pmic.200800951.

PMID:
19750512
35.

Identity of the growth-limiting nutrient strongly affects storage carbohydrate accumulation in anaerobic chemostat cultures of Saccharomyces cerevisiae.

Hazelwood LA, Walsh MC, Luttik MA, Daran-Lapujade P, Pronk JT, Daran JM.

Appl Environ Microbiol. 2009 Nov;75(21):6876-85. doi: 10.1128/AEM.01464-09. Epub 2009 Sep 4.

36.

Quantitative physiology of Saccharomyces cerevisiae at near-zero specific growth rates.

Boender LG, de Hulster EA, van Maris AJ, Daran-Lapujade PA, Pronk JT.

Appl Environ Microbiol. 2009 Sep;75(17):5607-14. doi: 10.1128/AEM.00429-09. Epub 2009 Jul 10. Erratum in: Appl Environ Microbiol. 2009 Dec;75(23):7578.

37.

An atypical PMR2 locus is responsible for hypersensitivity to sodium and lithium cations in the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D.

Daran-Lapujade P, Daran JM, Luttik MA, Almering MJ, Pronk JT, Kötter P.

FEMS Yeast Res. 2009 Aug;9(5):789-92. doi: 10.1111/j.1567-1364.2009.00530.x. Epub 2009 May 14.

38.

Energetic limits to metabolic flexibility: responses of Saccharomyces cerevisiae to glucose-galactose transitions.

van den Brink J, Akeroyd M, van der Hoeven R, Pronk JT, de Winde JH, Daran-Lapujade P.

Microbiology. 2009 Apr;155(Pt 4):1340-50. doi: 10.1099/mic.0.025775-0.

PMID:
19332835
39.

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data.

Knijnenburg TA, Daran JM, van den Broek MA, Daran-Lapujade PA, de Winde JH, Pronk JT, Reinders MJ, Wessels LF.

BMC Genomics. 2009 Jan 27;10:53. doi: 10.1186/1471-2164-10-53.

40.

Chemostat-based micro-array analysis in baker's yeast.

Daran-Lapujade P, Daran JM, van Maris AJ, de Winde JH, Pronk JT.

Adv Microb Physiol. 2009;54:257-311. doi: 10.1016/S0065-2911(08)00004-0. Review.

PMID:
18929070
41.

Dynamics of glycolytic regulation during adaptation of Saccharomyces cerevisiae to fermentative metabolism.

van den Brink J, Canelas AB, van Gulik WM, Pronk JT, Heijnen JJ, de Winde JH, Daran-Lapujade P.

Appl Environ Microbiol. 2008 Sep;74(18):5710-23. doi: 10.1128/AEM.01121-08. Epub 2008 Jul 18.

42.

Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design.

Fazio A, Jewett MC, Daran-Lapujade P, Mustacchi R, Usaite R, Pronk JT, Workman CT, Nielsen J.

BMC Genomics. 2008 Jul 18;9:341. doi: 10.1186/1471-2164-9-341.

43.

Saccharomyces cerevisiae SFP1: at the crossroads of central metabolism and ribosome biogenesis.

Cipollina C, van den Brink J, Daran-Lapujade P, Pronk JT, Porro D, de Winde JH.

Microbiology. 2008 Jun;154(Pt 6):1686-99. doi: 10.1099/mic.0.2008/017392-0.

PMID:
18524923
44.

New insights into the Saccharomyces cerevisiae fermentation switch: dynamic transcriptional response to anaerobicity and glucose-excess.

van den Brink J, Daran-Lapujade P, Pronk JT, de Winde JH.

BMC Genomics. 2008 Feb 27;9:100. doi: 10.1186/1471-2164-9-100.

45.

Revisiting the role of yeast Sfp1 in ribosome biogenesis and cell size control: a chemostat study.

Cipollina C, van den Brink J, Daran-Lapujade P, Pronk JT, Vai M, de Winde JH.

Microbiology. 2008 Jan;154(Pt 1):337-46. doi: 10.1099/mic.0.2007/011767-0.

PMID:
18174152
46.

Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes.

de Groot MJ, Daran-Lapujade P, van Breukelen B, Knijnenburg TA, de Hulster EA, Reinders MJ, Pronk JT, Heck AJ, Slijper M.

Microbiology. 2007 Nov;153(Pt 11):3864-78.

PMID:
17975095
47.

Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures.

De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ, Walker GM, Pronk JT, Daran JM, Daran-Lapujade P.

Appl Environ Microbiol. 2007 Dec;73(23):7680-92. Epub 2007 Oct 12.

48.

Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis.

Tai SL, Daran-Lapujade P, Walsh MC, Pronk JT, Daran JM.

Mol Biol Cell. 2007 Dec;18(12):5100-12. Epub 2007 Oct 10.

49.

The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels.

Daran-Lapujade P, Rossell S, van Gulik WM, Luttik MA, de Groot MJ, Slijper M, Heck AJ, Daran JM, de Winde JH, Westerhoff HV, Pronk JT, Bakker BM.

Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15753-8. Epub 2007 Sep 26.

50.

Control of the glycolytic flux in Saccharomyces cerevisiae grown at low temperature: a multi-level analysis in anaerobic chemostat cultures.

Tai SL, Daran-Lapujade P, Luttik MA, Walsh MC, Diderich JA, Krijger GC, van Gulik WM, Pronk JT, Daran JM.

J Biol Chem. 2007 Apr 6;282(14):10243-51. Epub 2007 Jan 24.

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